Microbiology
Nasopharyngeal samples were kept at 2-8°C and processed within 24 hours in the SARS-CoV2 cohort and 24 hours (up to 72 hours in weekends) in the influenza cohort.
In the influenza cohort, we used an RT-PCR system with microarray visualization (CLART PneumoVir, Genomica, Spain) capable of detecting adenovirus, bocavirus, coronavirus, rhinovirus, enterovirus, influenza virus A (subtypes AH3N2, AH1N1), influenza virus B, human metapneumovirus (subtypes A and B), parainfluenza virus 1, 2, 3, and 4 (subtypes A and B) and respiratory syncytial virus type A (RSV-A) and B (RSV-B), with a sensitivity of 83.3–100% depending on the virus. In the case of influenza, the sensitivity and specificity was 91% and 99% for influenza A, 82% and 99% for influenza B, respectively.8
Two different platforms were used for the detection of SARS-CoV2 throughout the duration of the study: TaqMan™ 2019-nCoV Assay Kit v1 (Thermo Fisher Scientific) and 2019 Novel Coronavirus (2019- nCoV) RNA (PCR-Fluorescence Probing) (Da An Gene Co. Ltd. Sun Yat-Sen University). RNA was extracted and purified from all samples using the QIAcube (QIAGEN) system and the QIAamp® Viral RNA mini kit (QIAGEN) following standard manufacturer procedure.